RetrogeneDB ID: retro_sscr_701

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:48911523..48911949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000011637
• Aliases: None
• Description: None

Sequence

>retro_sscr_701
AGTGGGAGCAGCCAAGCCTCAAGTTTGGTGGGCGGGTGGGCAGTAGGGCACGCGCACAGTGCCTGGCTGGGTGACTGTGC
AAACATAGGGGATGCCAGACCACAGGGGACGCAGGCCCCAGGCCCACCACCAAGGCTTTGACAAAGGAGGAAGATGAGTG
GAAAGATTTTTGAGCAAAAAGATGTTGGTTACACTGGCCTAAGAGTTCAAGCAATGCAAATAAGTGAAAAGAAAGATGAA
AATGGAAAGAGAGAAGATCCGGGTGATGAGTAGGAAGAAGGCGGAGGTGGTGAAGGAAAGTCTTTCCGTCAGTGGAAGAA
AACAGCTCCCGTACAAGCACCTCCTGCTTCAGTAGTTGTTTCAGAAACCCCAGAACCGACAGTAACTAGTAGCAGGTATA
GGCCTCCTGGGACCAGGTTGACCACA

Alignment

ORF - retro_sscr_701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66. %
• Parental protein coverage: 76.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGAARAASGSSGAASAAGGGAGAG--ARPGDGG-TTAAAGPGPATKALTKEEDEWKDF-EQKEVDYSGLR
          SG...A.S...G.A......A..G..A..GD...TT..AGP.P.TKALTKEEDEWKDF.EQK.V.Y.GLR
Retrocopy SGSSQASSLVGGWAVGHAHSAWLGDCANIGDAR<TTGDAGPRPTTKALTKEEDEWKDF>EQKDVGYTGLR

Parental  VQAMQISEKEEDENEKREDPGDNWEEGGGGGGGVGVEKSSGPWNKTAPVQAPPAPVVVSETPEPTMTSGV
          VQAMQISEK..DEN.KREDPGD..EE.GGGG.G....KS...W.KTAPVQAPPA.VVVSETPEPT.TS..
Retrocopy VQAMQISEKK-DENGKREDPGDE*EE-GGGGEG----KSFRQWKKTAPVQAPPASVVVSETPEPTVTSSR

Parental  YRPPGARLTT
          YRPPG.RLTT
Retrocopy YRPPGTRLTT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	1.86 RPM
SRP014902_testis	0.00 RPM	4.10 RPM
SRP018288_heart	0.00 RPM	5.19 RPM
SRP018288_kidney	0.00 RPM	10.84 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.00 RPM	1.53 RPM
SRP018856_adipose	0.00 RPM	20.58 RPM
SRP035408_brain	0.00 RPM	19.56 RPM
SRP035408_liver	0.00 RPM	9.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_701 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701 ,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta	ENSTSYG00000011401	2 retrocopies	retro_tsyr_1381, retro_tsyr_1759,